Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Wtap

Cell type

Cell type Class
Neural
Cell type
Neural Stem Cells
MeSH Description
Self-renewing cells that generate the main phenotypes of the nervous system in both the embryo and adult. Neural stem cells are precursors to both NEURONS and NEUROGLIA.

Attributes by original data submitter

Sample

source_name
Neural Stem Cell
cell line/type
mNSC
treatment
None
antibody
WTAP (Proteintech, 10200-1-AP)

Sequenced DNA Library

library_name
GSM5889179
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP, chromatin samples were incubated with specific antibodies in the ChIP Lysis buffer (20 mM Tris-HCl pH8.1, 150 mM NaCl, 2 mM EDTA, 1% TritonX-100 and 0.05% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on pre-washed protein A/G beads (20μl per reaction). The bound fractions were washed 3 times with the Lysis buffer, and twice with the Low Salt Wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP-40, 0.5% Na-deoxylcholate), and once with 10 mM Tris-HCl pH8.0. Elution and reverse crosslinking were carried out in the Elution buffer (50 mM Tris-HCl pH8.0, and 1% SDS) at 65℃ for 5 hours. After 1 hour of RNase A (1unit/μl) at 37℃ and Proteinase K (1unit/μl) digestion at 55℃, DNA samples were then purified using PCR extraction kit (QIAGEN #28006). For Cut&Tag seq, Hyperactive In-Situ ChIP Library Prep Kit for Illumina was performed according to the manual (Vazyme, TD902). The precipitated DNA samples were prepared for DNA deep sequencing according to manufacturer's guidelines (SWIFT, #21096).

Sequencing Platform

instrument_model
HiSeq X Ten

mm10

Number of total reads
13211328
Reads aligned (%)
39.1
Duplicates removed (%)
19.4
Number of peaks
50 (qval < 1E-05)

mm9

Number of total reads
13211328
Reads aligned (%)
39.1
Duplicates removed (%)
19.3
Number of peaks
36 (qval < 1E-05)

Base call quality data from DBCLS SRA